Publications & Media#

Papers and preprints#

Neuroinformatics Unit publications#

Ziminski, J. J., Sirmpilatze, N., Peri, B. D., Singh, S., Keshavarzi, S., Tyson, A. L. (2026) “datashuttle: automated data management for experimental neuroscience” Journal of Open Source Software 11(122), 9642, doi.org/10.21105/joss.09642

https://doi.org/10.21105/joss.09642

Sirmpilatze, N., Felder, A., Abdulazhanova, D., Schwigon, L., Tatarnikov, I., Haase, K., Musielak, I., Kobylkov, D., Margrie, T. W., Mouritsen, H., Heyers, D., Tyson, A. L., Weiler, S. (2026) “An open-source three-dimensional digital brain atlas of a migratory bird, the Eurasian blackcap” Current Biology 2025.03.04.641293, doi.org/10.1016/j.cub.2026.03.034

https://doi.org/10.1016/j.cub.2026.03.034

Felder, A., Chapuis, G., Tatarnikov, I., Sirmpilatze, N., Tyson, A. (2026). Mapping the state of neuroscientific software - a vision for collaboration beyond single institutes or labs (1.0). Zenodo, doi.org/10.5281/zenodo.19945701

https://doi.org/10.5281/zenodo.19945701

Duporge, I., Minano, S., Sirmpilatze, N., Tatarnikov, I., Wolf, S., Tyson, A. L., Rubenstein, D. (2025) “Tracking the Flight: Exploring a Computational Framework for Analyzing Escape Responses in Plains Zebra (Equus quagga)” arXiv 2505.16882, doi.org/10.48550/arXiv.2505.16882

https://doi.org/10.48550/arXiv.2505.16882

Domine, C. C. J., Carrasco-Davis, R., Hollingsworth L., Sirmpilatze, N., Tyson, A. L., Jarvis, D., Barry, C., Saxe, A. M. (2024) “NeuralPlayground: A Standardised Environment for Evaluating Models of Hippocampus and Entorhinal Cortex” bioRxiv, doi.org/10.1101/2024.03.06.583699

https://doi.org/10.1101/2024.03.06.583699

Publications relating to Neuroinformatics Unit software#

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022) “Accurate determination of marker location within whole-brain microscopy images” Scientific Reports, doi.org/10.1038/s41598-021-04676-9

https://doi.org/10.1038/s41598-021-04676-9

Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets” PLOS Computational Biology 17(5): e1009074, doi.org/10.1371/journal.pcbi.1009074

https://doi.org/10.1371/journal.pcbi.1009074

Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) “Visualizing anatomically registered data with Brainrender” eLife 2021;10:e65751, doi.org/10.7554/eLife.65751

https://doi.org/10.7554/eLife.65751

Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W., Portugues, R. (2020) “BrainGlobe Atlas API: a common interface for neuroanatomical atlases” Journal of Open Source Software 5(54), 2668, doi.org/10.21105/joss.02668

https://doi.org/10.21105/joss.02668